C1orf146

protein-coding

chromosome 1 open reading frame 146

Gene summary

Predicted to be involved in reciprocal meiotic recombination and synaptonemal complex assembly. Predicted to be active in chromosome. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_001012425.2

Inheritance

—

ClinVar variants

P:1U:3

Top phenotype

Male infertility

gnomAD constraint

pLI —, LoF o/e 0.67

Max pathogenic AF

—

Genomic locus

chr1:92,217,915-92,245,813

External References & Databases

Ensembl (ENSG00000203910)

Transcript & Mutation Effects

hg38 • Region Span ~27.9 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to C1orf146 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 1

Male infertilityTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001012425.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			2 clinvar			2
nonsense						0
start loss						0
frameshift		1 clinvar				1
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	1	3	0	0	4

Highest pathogenic variant AF is 0.0000041121857

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 9 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001012425.2	RefSeq	NP_001012425.1	5	MANE Select
ENST00000370375.8	Ensembl	ENSP00000359401.3	5	MANE Select
ENST00000370373.2	Ensembl	ENSP00000359399.2	3	Standard
ENST00000370373.3	Ensembl	ENSP00000359399.2	3	Standard

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000370375
Coding exons: 5
Length: 27874
Individuals with no LoFs: 125669
Homozygous LoFs: 0
Heterozygous LoFs: 27
Defined: 125696
p: 0.000107

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.397	78	88.5	0.881	0.00000396	1177
Missense (PolyPhen)		26	25.915	1.0033		359
Synonymous	1.07	21	28.2	0.744	0.00000122	331
Loss of Function	1.00	7	10.5	0.666	6.72e-7	118

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00019	0.00018	rare
Latino/Admixed American	0.00012	0.00012	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000054	0.000054	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00011	0.00011	rare
South Asian	0.00013	0.00013	rare
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.480
RVIS EVS: 0.1
RVIS percentile EVS: 61.28

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium